Research workbench
Structure of a MAPK pathway complex
Analyse Structure of a MAPK pathway complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6NYB
- Type
- protein
- Length
- 1,097 residues
- Chains
- 4
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- SERINE/THREONINE-protein kinase B-RAF; Dual specificity mitogen-activated protein kinase…
- EC
- 2.7.11.1, 2.7.12.2
- UniProt
- P15056, Q02750, V9P4T4
- Ligands
- AGS, ADP, LCJ, ZN, MG
- Pockets
- 13 · best druggability 0.82
Structure
electron microscopy · 3 distinct chains · 46% helix, 11% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | SERINE/THREONINE-protein kinase B-RAF (EC 2.7.11.1) | protein | 350 | 29% helix, 14% strand | P15056 |
| B | Dual specificity mitogen-activated protein kinase kinase 1 (EC 2.7.12.2) | protein | 289 | 44% helix, 17% strand | Q02750 |
| C, D | 14-3-3 protein zeta | protein | 229 | 77% helix, 0% strand | V9P4T4 |
Ligands and binding sites
- AGS · Phosphothiophosphoric acid-adenylate ester · ligand · chains A
- ADP · Adenosine-5'-diphosphate · ligand · chains B
- LCJ · 5-[(2-fluoro-4-iodophenyl)amino]-N-(2-hydroxyethoxy) imidazo[1,5-a]pyridine-6-carboxamide · ligand · chains B
- ZN · Zinc ion · metal · 2 copies · chains A
- MG · Magnesium ion · metal · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 709 | 0.82 | 0.86 | 77 | empty |
| 2 | 726 | 0.82 | 0.86 | 71 | ADP, MG, LCJ |
| 3 | 425 | 0.80 | 0.89 | 51 | empty |
| 4 | 865 | 0.77 | 0.80 | 80 | AGS |
| 5 | 253 | 0.72 | 0.87 | 37 | empty |
Interfaces
4 interfaces between chains.
- A–C · 1638 Ų buried · 14 hydrogen bonds · protein-protein
- A–D · 1329 Ų buried · 18 hydrogen bonds · protein-protein
- A–B · 1304 Ų buried · 11 hydrogen bonds · protein-protein
- C–D · 1064 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (phosphorylation).
Compared structures
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt P15056
- Every structure of UniProt Q02750
- Every structure of UniProt V9P4T4
- Elsewhere: RCSB PDB 6NYB · PDBe 6NYB · UniProt P15056 · UniProt Q02750 · UniProt V9P4T4
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